Structure of PDB 8hfr Chain B4 Binding Site BS01

Receptor Information

>8hfr Chain B4 (length=251) Species: 559292 (Saccharomyces cerevisiae S288C)

GRVIRNQRKGAGSIFTSHTRLRQGAAKLRTLDYAERHGYIRGIVKQIVHD
SGRGAPLAKVVFRDPYKYRLREEIFIANEGVHTGQFIYAGKKASLNVGNV
LPLGSVPEGTIVSNVEEKPGDRGALARASGNYVIIIGHNPDENKTRVRLP
SGAKKVISSDARGVIGVIAGGGRVDKPLLKAGRAFHKYRLKRNSWPKTRG
VAMNPVDHPHGGGNHQHIGKASTISRGAVSGQKAGLIAARRTGLLRGSQK
T

Ligand information

>8hfr Chain 1e (length=3274)

ugaccucaaaucagguaggaguacccgcugaacuuaagcauaucaauaag
cggaggaaaagaaaccaaccgggauugccuuaguaacggcgagugaagcg
gcaaaagcucaaauuugaaaucugguaccuucggugcccgaguuguaauu
uggagagggcaacuuuggggccguuccuugucuauguuccuuggaacagg
acgucauagagggugagaaucccguguggcgaggagugcgguucuuugua
aagugccuucgaagagucgaguuguuugggaaugcagcucuaagugggug
guaaauuccaucuaaagcuaaauauuggcgagagaccgauagcgaacaag
uacagugauggaaagaugaaaagaacuuugaaaagagagugaaaaaguac
gugaaauuguugaaagggaagggcauuugaucagacgccagcaucaguuu
ugguggcaggauaaauccauaggaauguagcuugccucgguaaguauuau
agccugugggaauacugccagcugggacugaggacugcgacguaagucaa
ggaugcuggcauaaugguuauaugccgcccgucuugaaacacggaccaag
gagucuaacgucuaugcgaguguuuggguguaaaacccauacgcguaaug
aaagugaacguagguuggggccucgcaagaggugcacaaucgaccgaucc
ugaugucuucggauggauuugaguaagagcauagcuguugggacccgaaa
gauggugaacuaugccugaauagggugaagccagaggaaacucuggugga
ggcucguagcgguucugacgugcaaaucgaucgucgaauuuggguauagg
ggcgaaagacuaaucgaaccaucuaguagcugguuccugccgaaguuucc
cucaggauagcagaagcucguaucaguuuuaugagguaaagcgaaugauu
agagguuccggggucgaaaugaccuugaccuauucucaaacuuuaaauau
guaagaaguccuuguuacuuaauugaacguggacauuugaaugaagagcu
uuuagugggccauuuuugguaagcagaacuggcgaugcgggaugaaccga
acguagaguuaaggugccggaauacacgcucaucagacaccacaaaaggu
guuaguucaucuagacagccggacgguggccauggaagucggaauccgcu
aaggaguguguaacaacucaccggccgaaugaacuagcccugaaaaugga
uggcgcucaagcguguuaccuauacucuaccgucaggguugauaugaugc
ccugacgaguaggcaggcguggaggucagugacgaagccuagaccguaag
gucgggucgaacggccucuagugcagaucuuggugguaguagcaaauauu
caaaugagaacuuugaagacugaaguggggaaagguuccacgucaacagc
aguuggacguggguuagucgauccuaagagauggggaagcuccguuucaa
aggccugauuuuaugcaggccaccaucgaaagggaauccgguuaagauuc
cggaaccuggauauggauucuucacgguaacguaacugaauguggagacg
ucggcgcgagcccugggaggaguuaucuuuucuucuuaacagcuuaucac
cccggaauugguuuauccggagauggggucuuauggcuggaagaggccag
caccuuugcuggcuccggugcgcuugugacggcccgugaaaauccacagg
aaggaauaguuuucaugccaggucguacugauaaccgcagcaggucucca
aggugaacagccucuaguugauagaauaauguagauaagggaagucggca
aaauagauccguaacuucgggauaaggauuggcucuaagggucggguagu
gagggccuuggucagacgcagcgggcgugcuuguggacugcuuggugggg
cuugcucugcuaggcggacuacuugcgugccuuguuguagacggccuugg
uaggucucuuguagaccgucgcuugcuacaauuaacgaucaacuuagaac
ugguacggacaaggggaaucugacugucuaauuaaaacauagcauugcga
uggucagaaagugauguugacgcaaugugauuucugcccagugcucugaa
ugucaaagugaagaaauucaaccaagcgcggguaaacggcguggauuaac
gagauucccacugucccuaucuacuaucuagcgaaaccacagccaaggga
acgggcuuggcagaaucagcggggaaagaagacccuguugagcuugacuc
uaguuugacauugugaagagacauagaggguguagaauaagugggagcuu
cggcgccagugaaauaccacuaccuuuauaguuucuuuacuuauucaaug
aagcggagcuggaauucauuuuccacguucuagcauucaaggucccauuc
ggggcugauccggguugaagacauugucagguggggaguuuggcuggggc
ggcacaucuguuaaacgauaacgcagauguccuaaggggggcucauggag
aacagaaaucuccaguagaacaaaaggguaaaagcccccuugauuuugau
uuucagugugaauacaaaccaugaaaguguggccuaucgauccuuuaguc
ccucggaauuugaggcuagaggugccagaaaaguuaccacagggauaacu
ggcuuguggcagucaagcguucauagcgacauugcuuuuugauucuucga
ugucggcucuuccuaucauaccgaagcagaauucgguaagcguuggauug
uucacccacuaauagggaacgugagcuggguuuagaccgucgugagacag
guuaguuuuacccuacugaugaauguuaccgcaauaguaauugaacuuag
uacgagaggaacaguucauucggauaauugguuuuugcggcugucugauc
aggcauugccgcgaagcuaccauccgcuggauuauggcugaacgccucua
agucagaauccaugcuagaacgcggugauuucuuugcuccacacaauaua
gauggauacgaauaaggcguccuuguggcgucgcugaaccauagcaggcu
agcaacggugcacuuggcggaaaggccuugggugcuugcuggcgaauugc
aaugucauuuugcguggggauaaaucauuuguauacgacuuagauguaca
acgggguauuguaagcaguagaguagccuuguuguuacgaucugcugaga
uuaagccuuuguugucugauuugu

.......................<<<<<<.....<<....>>......>>
>>>.>.........<<....>>..<<<<<......<<.....>>.....>
>>>>..<<<..<<.......<<.<<<<<<...>>>>>>.>>.......>>
....<<<<<<.<<<<<....<<<<<<<<<<<<<....<<<<......>>>
>.(.......<<<......)>>>..>.>>>>>>>>>..>>>........>
>>>>>>>>>>........<<<<<<<........>>>>>>>.....<<<<<
..((((((>>>>>..>>>................................
..<<....>>...............<<<<....>>>>.............
.....................<<<<<.<<<<<....<<<<<<<.<<<<<<
<<<<<<<<<.....<<<<<<<<<......<<<<........>>>>.....
..>>>>>>>.>.>.>>>>>.>>>>>>>>>>........<<<....>>>..
...>>>>>>>.....>>>>>.>>>>>..<<<<........>>>><<<<<<
....<<<<<<.<<<<<<..<<<...<<<<.....>>>>...>>>...<<.
...>>.......<<<<<..<<<<<....>>>>>...>>>>>.<<<<<<<<
...<<....>>...>>>.>>>.>>....>>>>>>.>>>>>>..<<.<..<
<<<<<<.....<<<<<<<<<..<<<....<<<<<<<....>>>>>>>...
..>>>...<<<..<<.<<........>>>>.>>>....>>>>>>>>>...
<<.......>>......>>>>>>...>..>.>>..<<<<<<....<.<<<
....>>>.><<<<<<<<<<...<<<.<<<<<<<.....<<<.........
..........<<<<<.....>>>>>................>>>.....>
>>>>...<<<<.<<<<.<......>>>>>.>>>>.....>>>>>.>>>>>
>>>.>>..<<<<.<<<<<.....>>>>>.>>>>....<<<......>>>.
..<<<<<<<..<<<<(((.....<<<<<<.....<<..........<<<.
<<<<<<<<<<.......<<<<<.<<<...<<.........>>...>>>..
.......<<......>>...>>>>>...>>>>>>>>>>>>>.........
.))).>>...>>>>>>.>>>>..>>>>>>><<<<<<<<<.........>>
>>>>>>>....>>>>>><.<<<<<<<<.<<......<<<<.<<<<....>
>>>>>>>...>>>>>>>>>>..>.....>>>>>><<.....<<.....<<
<<<<.......>>>>>><<<<.....<<<<<.<<...<<<<<<...<<..
...>>.>>>>>>....((<<<<<<...<<....<<<....>>>.......
..<<..............>>.....>>....>>...<<<<<........>
>>>>))<<<<.<<<<<<<.....<<<....>>>.......<<<<<<...<
<<<.<<<<<<<.<<<<<<<<<<..[[[..>>>>>><...<<<<<....<<
<<<<....<<<.....>>>....>>>>>>.....>>>>>....><<<<<<
<<....>>>>>>>>>>>>...>>>>>>>.>>>>.........>>>>>>..
........>>>..>>>>>>>>>>>>..>>.....<<......>>>>>>>.
<<<<.....>>>>..>>>>..<<<<.....<<<<<<<.<<.........<
.....<<<<<....<<..>>.....>>>>><<.<<<<<<<<.........
<<.....................<<<<<<<........<<<<.......<
.....>......>>>>........>>>>>>>...................
..<<<<<.....>>>>>.....>>..............>>..>>>>>>.>
>............<<<<<<<<<..<<<.........>>>..<<<<<<<..
..<<<<.....>>>>......>>>>>>>...<<<.<<<..<<<<<..<..
<<<.....<<<<....>>>>.....>>>>.>>>..>>>>>..>>>....>
>.>>>>>>>..>..>>.>>>>>>>..>>>>>>....>>....<<<<<...
.....>>>>>....<<<<<..<<<........<<<<<.<<<<<<..<<<<
<.<<<<<<<<..<<<<<<<<<<<<<<..<...........<<........
..................>>..>..>>>>.>>>>>>>>>>...<<<<<..
...<<<<..<<<<<......>>>>>...............<<<<<<....
>>>>>>..>>>>..>>>>>.....>>>>>>>>..>>>>>...<<<.....
>>>..<<<<<<...........>>>>>>..<<...<<<<<<<...<<<<<
<.......>>>>>>.....<<...(((>>....>>>>>>>...<<<.<<<
<<.......>>>>.>>>>.<<<....>>>.>>)))......<<<<<<<..
<<<<.))))))>>>>>>>>>>>.........>>>>..>>>>>>>......
........<<<<<....<.......>....>>>>>.............((
...<<<<.<<<<<<..<.<<<<<<<......>>>>>>>...>.<<<....
.))..>>>.....>>>>>..>...>>>>......<<<<<<<....>>>.>
>>>........>>>.>>>>>....<<<<<<<<..<<<<.<.<<<<<<...
............>>>>>>.><<<<<...<<<<....<<<<<<<<<<]]].
>>>>>..>>>>>...>>>>..>>>>>.<<<<...<<<<<...........
>>>>>...>>>>.>>>>....>>>>>>>>.......<<<<<..<<<....
...<<..........<<<<<<.....>>>>>>......>>.......<<<
<<<...<<<<<.<..<<<......>>>..>.>>>>>.>>>>>>.......
.........>>>..>>>>>..<<<<<.<.............>.....<<<
<<<<<<.<<<....<<<<.<..<<<<<......>>>>>..>>>>>...>>
>....>>>>.>>>>>..>>>>>..

Receptor-Ligand Complex Structure

Structure summary

• PDB: 8hfr Nuclear export of pre-60S particles through the nuclear pore complex.
• Resolution: 2.64 Å
• Binding residue (original residue number in PDB): G2 R3 V4 N7 Q8 R9 K10 G11 I15 T17 S18 H19 T20 R21 R23 G25 Y34 R37 Y40 I44 H50 R54 R64 Y67 K68 Y69 G85 F87 Y89 A94 S95 A125 L126 A127 R128 A129 S130 N132 L150 S152 K156 R174 K177 L179 L180 K181 A182 G183 H187 L191 R193 W196 K198 T199 R200 G201 V202 M204 N205 P206 V207 D208 H211 G213 G214 N215 H216 A222 S223 T224 I225 R227 V230 S231 Q233 K234 G236 A239 A240 R241 R242 T243 G244 L245 L246 Q250
• Binding residue (residue number reindexed from 1): G1 R2 V3 N6 Q7 R8 K9 G10 I14 T16 S17 H18 T19 R20 R22 G24 Y33 R36 Y39 I43 H49 R53 R63 Y66 K67 Y68 G84 F86 Y88 A93 S94 A124 L125 A126 R127 A128 S129 N131 L149 S151 K155 R173 K176 L178 L179 K180 A181 G182 H186 L190 R192 W195 K197 T198 R199 G200 V201 M203 N204 P205 V206 D207 H210 G212 G213 N214 H215 A221 S222 T223 I224 R226 V229 S230 Q232 K233 G235 A238 A239 R240 R241 T242 G243 L244 L245 Q249

Gene Ontology

Molecular Function

• GO:0003723 RNA binding
• GO:0003735 structural constituent of ribosome
• GO:0019843 rRNA binding

Biological Process

• GO:0002181 cytoplasmic translation
• GO:0006412 translation
• GO:0042273 ribosomal large subunit biogenesis
• GO:1990145 maintenance of translational fidelity

Cellular Component

• GO:0005737 cytoplasm
• GO:0005829 cytosol
• GO:0005840 ribosome
• GO:0022625 cytosolic large ribosomal subunit
• GO:0022626 cytosolic ribosome
• GO:1990904 ribonucleoprotein complex

External links

• PDB: RCSB:8hfr, PDBe:8hfr, PDBj:8hfr
• PDBsum: 8hfr
• PubMed: 37258668
• UniProt: P0CX45|RL2A_YEAST Large ribosomal subunit protein uL2A (Gene Name=RPL2A)